Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005713.1 Corchorus capsularis cultivar CVL-1 contig05731, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6715
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:956 original size:321 final size:320
Alignment explanation
Indices: 7--1628 Score: 1828
Period size: 321 Copynumber: 5.0 Consensus size: 320
1 CGGTTT
* * * * * *
7 TTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTACATGATTTTTGAC-GCAAAGATT
1 TTTTTGGCTAAAAACGCGTTTCGGGGTCCCAACTCAGTTTTGCATGATTTTTGGCAG-AAAGACT
* * **
71 CCTTGAAATATTTATAATAATCTAACCAAATCTCAATCACATTGGATTTAAGGATTTGTTTTTAC
65 CCTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
* * * *
136 GAGCATCTGAATCTTGTTTCGATTTAATAAAAAATTAA-TCTG-AAAAAATGGAAAAACGATATT
130 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATT
* * * *
199 AGAAACGTGAAAAACCCTTCAATTTTTTGGTGTTAAATTATATATTTATTCTGAATATTATGGCA
195 AGAAACGTGAAAAACCCTTCAATTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCA
* **
264 AAAAATTTGGAAAAAACTTTTCGGGTCAGTTTTAGTCGAAATCAAGTACTAACCATCACGG
260 AAAAATTTGGAAAAAACTTTTCGGGTCAGTTTTAGCCGAAATCGTGTACTAACCATCACGG
* * * * * * * **
325 TTTTTGGCTAAAAACACGTTT-TGGATTCCGACTTAGTTTTACATGATTTTTAACAGAAAGACTC
1 TTTTTGGCTAAAAACGCGTTTCGGGGTCCCAACTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
* * ** *
389 CTTGAAGTATCTATATTCATCTAAATAAATCAT-AGCCACATTGGATTTAAAGATTTGTTTTTAC
66 CTTGAAATATCTATAATCATCTAACCAAATC-TCAGCCACATTGGATTTAAGGATTTGTTTTTAC
* * * *
453 GACCATCTGAATTTTGATTCGATTTAATTAGAAATAAATTCGG-GAAAAATGG-AAAACGATATT
130 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATT
* *** * *
516 A-AAAGTGTGAAAAACCCTTCAATTTTTTGACCTTGAATTAAATATTTTATCTGAGTATTGTGGC
195 AGAAA-CGTGAAAAACCCTTCAATTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGC
** * * *
580 AAAAAATTGTGGAAAAAAAATTTCGAGTCAGTTTTAGCCTAAATCGTGTACTAACCATCATGG
259 AAAAAATT-TGGAAAAAACTTTTCGGGTCAGTTTTAGCCGAAATCGTGTACTAACCATCACGG
* * *** ** *
643 TTTTTTGCTGAAAACGTAATTCGGGGTTTCAACTCAGTTTTGCATGGA-TTTTGGCATAAAGACT
1 TTTTTGGCTAAAAACGCGTTTCGGGGTCCCAACTCAGTTTTGCAT-GATTTTTGGCAGAAAGACT
* * * *
707 CCATGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGCATTTAGGGATTTGTTTTTAA
65 CCTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
* * *
772 GAGCATCTCAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATTTG-AAAACGATAA
130 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAA-TGGAAAAACGATAT
* *
836 TAGAAACGTGAAAAACCCTTCAATTTTTTGGTGTTGAATTATATATTTTTTCTGAGCATTGTGGT
194 TAGAAACGTGAAAAACCCTTCAATTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* * * *
901 AAAAAATTTTGAGAAAACTTTTCGGGTAAGTTTTAGCCGAAAATCGTGCACTAACCATCACGG
259 AAAAAATTTGGAAAAAACTTTTCGGGTCAGTTTTAGCCG-AAATCGTGTACTAACCATCACGG
* * *
964 TTTTTGGCTAAAAACGCGTTTC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAATACTC
1 TTTTTGGCTAAAAACGCGTTTCGGGGTCCCAACTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
* * * * *
1028 CTTGAAATATCTATACTTATCTAACCAAATCTCAGCCACATTAGATTTAATGATTTGTTTATACG
66 CTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* * * *
1093 AGCATCTGAATCTTGTTTTGATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAACTATATTA
131 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTA
* ** * **
1158 GAAGCAAG-AAAATCCTGTCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATCATGGC
196 GAAACGTGAAAAACCCT-TCAAT-TTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* * * * *
1222 AAAAAA-TTGAGAAAAAAATTTTCAGATCAGTTTTTGGCCGAAATCGTGTACTAACCATCACAG
259 AAAAAATTTG-GAAAAAACTTTTCGGGTCAG-TTTTAGCCGAAATCGTGTACTAACCATCACGG
* * *
1285 TTTTT-GCTAAAAACGCGTTTTGGGG-CCCTAACTTAGTTTTGCATGATCTTTT-GAAGAAAGAC
1 TTTTTGGCTAAAAACGCGTTTCGGGGTCCC-AACTCAGTTTTGCATGAT-TTTTGGCAGAAAGAC
* * * *
1347 ACCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGTAATTAAGGA-TT-TTTTTA
64 TCCTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * *
1410 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-AAAAAAACATGGAAAAATGGTA
129 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAA-ATGGAAAAACGATA
*** * ** * *
1474 TTAGAAGTATGAAAAATCCTTCAATTTTTTTATCGTTGAATTATATACTTTTTCTGAGTATTGTC
193 TTAGAAACGTGAAAAACCCTTCAATTTTTTGGT-GTTGAATTATATATTTTTTCTGAGTATTGTG
* *
1539 GCAAAAAA-AT-GAGAAAAACTTTTCGGGTCAGTTTTTGCAGAATTTTAGCCGAAATCGTGTACA
257 GCAAAAAATTTGGA-AAAAACTTTTC-GG---G----T-CAG--TTTTAGCCGAAATCGTGTACT
1602 AACCATCACGG
310 AACCATCACGG
1613 TTTTTGGCTAAAAACG
1 TTTTTGGCTAAAAACG
1629 TGTTCCGGAG
Statistics
Matches: 1096, Mismatches: 172, Indels: 61
0.82 0.13 0.05
Matches are distributed among these distances:
316 3 0.00
317 190 0.17
318 116 0.11
319 240 0.22
320 215 0.20
321 269 0.25
322 15 0.01
326 1 0.00
327 3 0.00
328 34 0.03
329 10 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (320 bp):
TTTTTGGCTAAAAACGCGTTTCGGGGTCCCAACTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
CTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTA
GAAACGTGAAAAACCCTTCAATTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAA
AAAATTTGGAAAAAACTTTTCGGGTCAGTTTTAGCCGAAATCGTGTACTAACCATCACGG
Found at i:1417 original size:639 final size:636
Alignment explanation
Indices: 7--1573 Score: 1956
Period size: 639 Copynumber: 2.5 Consensus size: 636
1 CGGTTT
** * * *
7 TTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTACATGATTTTTGACGCAAAGATTC
1 TTTTTTGCTAAAAACGCGTTTCGGGGCCCTAACTCAGTTTTGCATGATTTTTGAAG-AAAGACTC
* * ** *
72 CTTGAAATATTTATAATAATCTAACCAAATCTCAATCACATTGGATTTAAGGATTTGTTTTTACG
65 CTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACG
* * *
137 AGCATCTGAATCTTGTTTCGATTTAATAAAAAATTAA-TCTG-AAAAAATGGAAAAACGATATTA
130 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GAAAAAAATGGAAAAACGATATTA
* * * *
200 GAAACGTGAAAAACCCTTCAATTTTTTGGTGTTAAATTATATATTTATTCTGAATATTATGGCAA
194 GAAACGTGAAAAACCCTTCAATTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAA
* * * *
265 AAAATTTGGAAAAAACTTTTCGGGTCAGTTTTAGTCGAAATCAAGTACTAACCATCACGGTTTTT
259 AAAATTTTGAGAAAACTTTTCGGGTCAGTTTTAGCCGAAATCAAGCACTAACCATCACGGTTTTT
* ** *
330 GGCTAAAAACACGTTTTGGATTCCGACTTAGTTTTACATGATTTTTAACAGAAAGACTCCTTGAA
324 GGCTAAAAACACGTTTCGGACCCCGACTCAGTTTTACATGATTTTTAACAGAAAGACTCCTTGAA
* * * *
395 GTATCTATATTCATCTAAATAAATCATAGCCACATTGGATTTAAAGATTTGTTTTTACGACCATC
389 ATATCTATATTCATCTAAACAAATCATAGCCACATTAGATTTAAAGATTTGTTTATACGACCATC
* * * ***
460 TGAATTTTGATTCGATTTAATTAGAAATAAATTCGGGAAAAATGGAAAACGATATTAAAAGTGTG
454 TGAATCTTGATTCGATTTAATTAAAAATAAATTCGGAAAAAATGGAAAACGATATTAAAAGCAAG
**
525 AAAAACCCTTCAATTTTTTGACCTTGAATTAAATATTTTATCTGAGTATTGTGGCAAAAAATTGT
519 AAAAACCCTTCAATTTTTTGACCTTGAATTAAATATTTTATCTGAGTATCATGGCAAAAAATTGT
* * **
590 GGAAAAAAAATTTCGAGTCAGTTTTAGCCTAAATCGTGTACTAACCATCATGG
584 AGAAAAAAAATTTCGAGTCAGTTTTAGCCGAAATCGTGTACTAACCATCACAG
* *** ** * * *
643 TTTTTTGCTGAAAACGTAATTCGGGG-TTTCAACTCAGTTTTGCATGGATTTTGGCATAAAGACT
1 TTTTTTGCTAAAAACGCGTTTCGGGGCCCT-AACTCAGTTTTGCAT-GATTTTTGAAGAAAGACT
* * *
707 CCATGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGCATTTAGGGATTTGTTTTTAA
64 CCTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTAC
* * *
772 GAGCATCTCAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATTTG-AAAACGATAA
129 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GAAAAAAA-TGGAAAAACGATAT
* *
836 TAGAAACGTGAAAAACCCTTCAATTTTTTGGTGTTGAATTATATATTTTTTCTGAGCATTGTGGT
192 TAGAAACGTGAAAAACCCTTCAATTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* **
901 AAAAAATTTTGAGAAAACTTTTCGGGTAAGTTTTAGCCGAAAATCGTGCACTAACCATCACGGTT
257 AAAAAATTTTGAGAAAACTTTTCGGGTCAGTTTTAGCCG-AAATCAAGCACTAACCATCACGGTT
* * * ** *
966 TTTGGCTAAAAACGCGTTTCGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAATACTCCTT
321 TTTGGCTAAAAACACGTTTCGGACCCCGACTCAGTTTTACATGATTTTTAACAGAAAGACTCCTT
* *
1031 GAAATATCTATACTT-ATCTAACCAAATC-TCAGCCACATTAGATTTAATGATTTGTTTATACGA
386 GAAATATCTATA-TTCATCTAAACAAATCAT-AGCCACATTAGATTTAAAGATTTGTTTATACGA
* * * * * *
1094 GCATCTGAATCTTGTTTTGATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAACTATATTAG
449 CCATCTGAATCTTGATTCGATTTAATTAAAAATAAATTCGG-AAAAAATGG-AAAACGATATTAA
* *** * *
1159 AAGCAAG-AAAATCCTGTCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATCATGGCA
512 AAGCAAGAAAAACCCT-TCAAT-TTTTTGACCTTGAATTAAATATTTTATCTGAGTATCATGGCA
* *
1223 AAAAATTG-AGAAAAAAATTTTC-AGATCAGTTTTTGGCCGAAATCGTGTACTAACCATCACAG
575 AAAAATTGTAGAAAAAAAATTTCGAG-TCAG-TTTTAGCCGAAATCGTGTACTAACCATCACAG
* * *
1285 -TTTTTGCTAAAAACGCGTTTTGGGGCCCTAACTTAGTTTTGCATGATCTTTTGAAGAAAGACAC
1 TTTTTTGCTAAAAACGCGTTTCGGGGCCCTAACTCAGTTTTGCATGAT-TTTTGAAGAAAGACTC
* * *
1349 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGTAATTAAGGA-TT-TTTTTACG
65 CTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACG
* * *
1412 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAAAAAAACATGGAAAAATGGTATTA
130 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAA-ATGGAAAAACGATATTA
*** * ** * *
1477 GAAGTATGAAAAATCCTTCAATTTTTTTATCGTTGAATTATATACTTTTTCTGAGTATTGTCGCA
194 GAAACGTGAAAAACCCTTCAATTTTTTGGT-GTTGAATTATATATTTTTTCTGAGTATTGTGGCA
*
1542 AAAAA--ATGAGAAAAACTTTTCGGGTCAGTTTT
258 AAAAATTTTGAG-AAAACTTTTCGGGTCAGTTTT
1574 TGCAGAATTT
Statistics
Matches: 791, Mismatches: 120, Indels: 37
0.83 0.13 0.04
Matches are distributed among these distances:
636 132 0.17
637 10 0.01
638 122 0.15
639 266 0.34
640 59 0.07
641 130 0.16
642 72 0.09
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (636 bp):
TTTTTTGCTAAAAACGCGTTTCGGGGCCCTAACTCAGTTTTGCATGATTTTTGAAGAAAGACTCC
TTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGA
GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAAACGATATTAGA
AACGTGAAAAACCCTTCAATTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAA
AATTTTGAGAAAACTTTTCGGGTCAGTTTTAGCCGAAATCAAGCACTAACCATCACGGTTTTTGG
CTAAAAACACGTTTCGGACCCCGACTCAGTTTTACATGATTTTTAACAGAAAGACTCCTTGAAAT
ATCTATATTCATCTAAACAAATCATAGCCACATTAGATTTAAAGATTTGTTTATACGACCATCTG
AATCTTGATTCGATTTAATTAAAAATAAATTCGGAAAAAATGGAAAACGATATTAAAAGCAAGAA
AAACCCTTCAATTTTTTGACCTTGAATTAAATATTTTATCTGAGTATCATGGCAAAAAATTGTAG
AAAAAAAATTTCGAGTCAGTTTTAGCCGAAATCGTGTACTAACCATCACAG
Found at i:2295 original size:319 final size:318
Alignment explanation
Indices: 1850--4716 Score: 1941
Period size: 319 Copynumber: 8.9 Consensus size: 318
1840 TGATCACGGT
* * * * **
1850 TTTTTTGCTAAAATCGCGATTCGGGGCCTCGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTC
1 TTTTTTGCTAAAAACGCGTTTCGGAGCCCCGACTCAGTTTTGCATGGTTTTTGGCGCAAAGACTC
* * * *
1915 CTGGAAATATCTATAATCATCTAACCAAAAT-TCAGCCACATTGAATTTAAGGATATGTTTTTAC
66 CTTGAAATATCTATATTCATCTAACC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
*
1979 GAGCATCTGAATCTTGTTTCGATTTAATTAG-AATAAATTCGGAAAAAAAAGGAAAACTATATTA
130 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGAAAACGATATTA
* *
2043 GAAGCGTGAAAAACCCTTAAACTTTTTTGGCATTGAATTATATACTTTTTT-TGAGTATTGTGGG
195 GAAGCGTGAAAAACCCTTAAA-TTTTTTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGC
*
2107 AAAAAATTGAGGAAAAACTATTCGGGTCAGTTTTTGCAAAAAT-ATAGCCAAAATCGTTGG
258 AAAAAATTGAGGAAAAACTATTCGGGTCAATTTTTGCAAAAATCATAGCCAAAATCGTTGG
* * * * * * ** *
2167 TTTTTTTTGCTAAATACGCGTTCCGAAGTCCCTACTCAATTTCACATGTTTTTTGGCGCAAAGAC
1 --TTTTTTGCTAAAAACGCGTTTCGGAGCCCCGACTCAGTTTTGCATGGTTTTTGGCGCAAAGAC
* * *
2232 ACCTTGAAATATCTATATTCAT-TGATCCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTT
64 TCCTTGAAATATCTATATTCATCT-AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * * * * *
2296 ACGTGTATCTAAATCTTGTTTCGATTTAATTAGAAATTAATAC-GAAAAAAATGGAAAAACGATA
128 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGG-AAAACGATA
* ** * * * * *
2360 TTATAAGCAAGAAAATCCCGTCAATTTTTTGGTGTTGAATTATATA-TTTTTCTGAGTATCGTGG
192 TTAGAAGCGTGAAAAACCCTTAAATTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG
* ** * * * ** * * * * *
2424 CAAAAAATTGAGAAAAAAAAATTTCAGATCAGTTTTTAGCTGAAATCGTGGACTAACCATC-ATG
257 CAAAAAATTGAGGAAAAACTA-TTCGGGTCAATTTTT-GCAAAAATCATAG-CCAA-AATCGTTG
2488 G
318 G
** * * * *
2489 TTTTAGGCCT-AAAACGCTTTTC-TAGGCCCCGACTTAGTTTTGCATGATTTTTGGCAG-AAAGA
1 TTTTTTG-CTAAAAACGCGTTTCGGA-GCCCCGACTCAGTTTTGCATGGTTTTTGGC-GCAAAGA
* * * * *
2551 TTCCTTGAAATATCTATATTTATCTAACAAAATCTTAGCCACATTGTATTTAAGGATTTGTTTTT
63 CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* ** *
2616 ACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTAGAAAAACATAGGAAAACGATA
128 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAA-AAAGGAAAACGATA
* * * * * * *
2681 TTTGAAGCGTGAAAAAACCCCTCAAA-TTTTTGTCGTTGAAGTACATATTTTTTCTGAATATAGT
192 TTAGAAGCGTG-AAAAA-CCCTTAAATTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGT
* ** * * ** *
2745 GCCAAAAAAAATTGAGGAAATTCTTTTCGGGTCAGTTTTTGC-AAAATTTTAGCCGAAATCTTGT
255 GGC--AAAAAATTGAGGAAAAACTATTCGGGTCAATTTTTGCAAAAATCATAGCCAAAATC--G-
2809 ATTAACCATCACGG
315 --T-----T---GG
* * * * *
2823 TTTTTGGCTAAAAACGCGTTCCGCAG--CC-A--C-G-GTTG-A---ATTTT---GC-AAGACTC
1 TTTTTTGCTAAAAACGCGTTTCGGAGCCCCGACTCAGTTTTGCATGGTTTTTGGCGCAAAGACTC
** * * * * * *
2873 CTCCAAATATTTATATTTATCGAACCAAATCTCAGCCACATTAGATATAAGGATTT-ATTTTACG
66 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* * * * *
2937 AGCATCTGAATTTTGTTTCGATTAAATTAGAAATTAATTCAGAGAAAAATCAA--AAAACAATAT
131 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-G-GAAAAA-AAAGGAAAACGATAT
* * * *
3000 TAGAAGCGTG-AAAATCCTGACAATCTTTTTGGCGTAGAATTATGTATTTTTTCTGAGTATTGTG
193 TAGAAGCGTGAAAAACCCTTA-AAT-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTG
* * * * * * ** * *
3064 GCAAAGAATTGAGAAAAAAGTTTTCGCGTCAATTCTTAGCTGAAATCGT-G---TAA--GTTACG
256 GCAAAAAATTGAGGAAAAACTATTCGGGTCAATT-TTTGCAAAAATCATAGCCAAAATCGTT--G
*
3123 A
318 G
* * * * * **
3124 TTTTTTCCTAAAAACACGTTTC-GAGGCCAC-TCTCAGTTTTGCATGGTTTTTGACATATAA-AC
1 TTTTTTGCTAAAAACGCGTTTCGGA-GCCCCGACTCAGTTTTGCATGGTTTTTGGCGCA-AAGAC
* * * * *
3186 TACTTGAAATATCTAAAATCATCTAACCAAATATCAGCGACATTGGATTTAAGGATTTGTTTTTA
64 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * *
3251 CGAGCATCTAAATCTTGTTTCGATTTAATTA-AAA-AATTATTTGGAAAAAAAGGGAAAACTG-T
129 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA--ATTCGGAAAAAAAAGGAAAAC-GAT
* * * *
3313 ATTAGAAGCGTGAAAAATCCTTAAACTTTTTTGGTGTTGAATTATATAATTTTTCTGAATATTGT
191 ATTAGAAGCGTGAAAAACCCTTAAA-TTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGT
* * * *
3378 TGTAAAAAATTGAGGAAAAACTATTCGGGTCAGTTTTTGCAAAAAT-AT-GCCTGAAATCGTACC
255 GGCAAAAAATTGAGGAAAAACTATTCGGGTCAATTTTTGCAAAAATCATAGCC-AAAATCGT---
3441 ATCACGG
316 -T---GG
* * * * * * **
3448 TTTTTTGCTAAAAACGCGTTTTGGAGTCCCGACTCAATTTTGCAAGATTTTTGGCACAAAGGTTC
1 TTTTTTGCTAAAAACGCGTTTCGGAGCCCCGACTCAGTTTTGCATGGTTTTTGGCGCAAAGACTC
* * *
3513 CTTGAAATTTCTATATTCATCGAACCAAATCTCAGCTACA-TGAGATTTAA-GATTTGTTTTTAC
66 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTG-GATTTAAGGATTTGTTTTTAC
** * ** **
3576 GTCCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCATAAAAAATGAAAAAAAACGATAT
130 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAA--AAGGAAAACGATAT
* ** * * * ** * * * *
3641 TAGAAACAAGAAAATCCCATCAATCTTTTCCGCGTTAAATTATATATTTTTTATGAGTATCGTAG
193 TAGAAGCGTGAAAAACCCTTAAAT-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG
* * * *
3706 CAAAAAAATTGA-TAAAAAC-ATTTCGGGTCAAATTTTAGGC-AAAATCGAGTA-CTAACCATC-
257 C-AAAAAATTGAGGAAAAACTA-TTCGGGTC-AATTTT-TGCAAAAATC-A-TAGCCAA-AATCG
**
3766 ACGG
315 TTGG
* * * * * * **
3770 TTTATGGCTAGAAACGCGTTTCGGAGCCCCGACTTAGTTTTGCTTGTTTTTTAGTAG-AAAGACT
1 TTTTTTGCTAAAAACGCGTTTCGGAGCCCCGACTCAGTTTTGCATGGTTTTT-GGCGCAAAGACT
* * * * * *
3834 -ATTTATAATATCTATATTCATCTAACTAAATCTCAGCCACATTGTATTTAAGAATTTGGTTTTA
65 CCTTGA-AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * * * *
3898 CAATCATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAACATGGAAAACGATATT
129 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGAAAACGATATT
* * * * *
3963 AGAAGCGGGAAAAACCCTTCAATTTTTTTGTCGTTGAATTATATATATATTTTCTGAGTACTATG
194 AGAAGCGTGAAAAACCCTT-AAATTTTTTGGCGTTGAATTATATAT-T-TTTTCTGAGTATTGTG
* * * * * * ** * *
4028 GTAAAAAATTGAGGAAAAGCTTTTCAGGTAAATTCTTGC-AAAATTTTAGTCGAAATCGTGTACT
256 GCAAAAAATTGAGGAAAAACTATTCGGGTCAATTTTTGCAAAAATCATAGCCAAAATC--G---T
*
4092 AACCATCACGA
316 -----T---GG
** * * * * * * *
4103 TTTTTTGCT-AAAACTTGTTCCGGAGCCCCAACTTAATTTTGCATGATTTTTTGCGCAAAGTCTC
1 TTTTTTGCTAAAAACGCGTTTCGGAGCCCCGACTCAGTTTTGCATGGTTTTTGGCGCAAAGACTC
** * *
4167 CTCAAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTG-TTTTACG
66 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* ** * * * *
4231 AGAATCTGAATAATGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATATGGAAAAACAATATT
131 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAA-AAGG-AAAACGATATT
* ** * * * * *
4296 AGAAGCGTGAAAATCCAGTCAGTCTTTTTGGCGTAGAATTATTTATTTTTTCTGAGTATCGTGGC
194 AGAAGCGTGAAAAACCCTTAAAT-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* * ** * *
4361 AAAAAATTGA-GAAAATGCT-TTCGTGTCAATTTTTAGCTGAAATCGT-G----TA-CGTTACGG
258 AAAAAATTGAGGAAAA-ACTATTCGGGTCAATTTTT-GCAAAAATCATAGCCAAAATCGTT--GG
** *
4418 -TTTTTGCCTAAAAACGCGTTTCGGAGCCCCGACTCAGTTTTGCATGGTTTTTGGCATAAAAACT
1 TTTTTTG-CTAAAAACGCGTTTCGGAGCCCCGACTCAGTTTTGCATGGTTTTTGGCGCAAAGACT
* * *
4482 ACTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACATTGGATTTTTAAAGATTTGTTTTT
65 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA--TTTAAGGATTTGTTTTT
* **** *
4547 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAGTTTTTTTTTTAAAAAAA-GAAAACA
128 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA----ATTCGGAAAAAAAAGGAAAACG
* * * *
4611 AT-TTCAGAAGCATGAAAAACCCTTTAATTTTTTTCGCGTTGAATTATATATTCTTT-TGAGTAT
189 ATATT-AGAAGCGTGAAAAACCC-TTAAATTTTTTGGCGTTGAATTATATATTTTTTCTGAGTAT
* * * * ** *
4674 TATGGTAAAGAATTGCGGAAAAAAAATTTTGGGTCAATTTTTG
252 TGTGGCAAAAAATTGAGGAAAAACTA-TTCGGGTCAATTTTTG
4717 TTTCAAGGAG
Statistics
Matches: 1962, Mismatches: 441, Indels: 289
0.73 0.16 0.11
Matches are distributed among these distances:
300 1 0.00
301 22 0.01
302 1 0.00
303 1 0.00
305 1 0.00
306 1 0.00
307 4 0.00
308 1 0.00
310 1 0.00
311 4 0.00
313 3 0.00
314 23 0.01
315 141 0.07
316 163 0.08
317 12 0.01
318 141 0.07
319 292 0.15
320 234 0.12
321 102 0.05
322 141 0.07
323 117 0.06
324 92 0.05
325 85 0.04
326 73 0.04
327 24 0.01
328 3 0.00
329 2 0.00
330 21 0.01
331 79 0.04
332 101 0.05
333 56 0.03
334 19 0.01
335 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (318 bp):
TTTTTTGCTAAAAACGCGTTTCGGAGCCCCGACTCAGTTTTGCATGGTTTTTGGCGCAAAGACTC
CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGAAAACGATATTAG
AAGCGTGAAAAACCCTTAAATTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAA
AAATTGAGGAAAAACTATTCGGGTCAATTTTTGCAAAAATCATAGCCAAAATCGTTGG
Found at i:4279 original size:654 final size:644
Alignment explanation
Indices: 1637--4696 Score: 2832
Period size: 639 Copynumber: 4.8 Consensus size: 644
1627 CGTGTTCCGG
* * *
1637 AGCCACATTGTA-ATTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAA
1 AGCCACATTGGATA-TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * ** * * * * * * * * *
1701 ATAAATTCGGAAAAAAATGGAAAACAATATCAAAAGCATGAAAAACTCTTTAAT-TTTTTAGCAT
65 ATTAATTCAG-AAAAAATAAAAAACAATATTAGAAGCAAGAAAATCCCATCAATCTTTTTGGCGT
* * * * *
1765 TGAATTATATATTTTTTTCTGAGTATTGTGGCAAAGAATTGCGGGAAAAA-A-TT-GGGTC-AGT
129 AGAATTATATA-TTTTTTCTGAGTATCGTGGCAAAAAATT--GAGAAAAACATTTCGGGTCAAAT
* * * * *
1826 TTTAGCCGAAATCGTG------ATCACGGTTTTTTTG-CTAAAATCGCGATTCGGGGCCTCGACT
191 TTTAGCTGAAATCGTGTACTAAATCACGG--TTTTTGCCTAAAAACGCGTTTC-GAGCCCCGACT
* * * * *
1884 CAGTTTTGCATGGTTTTTGGCATAAAGACTCCTGGAAATATCTATAATCATCTAACCAAAAT-TC
253 TAGTTTTGCATGGTTTTTGGCAGAAAAACTACTTGAAATATCTATAATCATCTAA-CAAAATCTC
* *
1948 AGCCACATTGAATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-AA
317 AGCCACATTGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* * * * * *
2012 TAAATTCGGAAAAAAAAGGAAAACTATATTAGAAGCGTGAAAAACCCTTAAACTTTTTTGGCATT
382 TAAATTCGGAAAAAAATGGAAAACGATATTAGAAGCGGGAAAAACCCTTAAATTTTTTTGTCGTT
* * *
2077 GAATTATATACTTTTTT-TGAGTATTGTGGGAAAAAATTGAGGAAAAACTATTCGGGTCAGTTTT
447 GAATTATATA-TTTTTTCTGAATATTATGGTAAAAAATTGAGGAAAAACTATTCGGGTCAGTTTT
* * * *
2141 TGCAAAAATATAGCCAAAATCGT-TGGT----T-----TTTTTTGCTAAATACGCGTTCCGAAGT
511 TGCAAAAATATAGCCGAAATCGTGT-ATACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGT
** * * * *
2196 CCCTACTCAATTTCACATG-TTTTTTGGCGCAAAGACACCTTGAAATATCTATATTCATTGATCC
575 CCC-ACTCAATTTTGCATGATTTTTT-GCGCAAAGACTCCTCGAAATATCTATATTCATCGAACC
2260 AAATCTC
638 AAATCTC
* * *
2267 AGCCACATTGGATATAAGGATTTGTTTTTACGTGTATCTAAATCTTGTTTCGATTTAATTAGAAA
1 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* * * * * *
2332 TTAATAC-GAAAAAAATGGAAAAACGATATTATAAGCAAGAAAATCCCGTCAAT-TTTTTGGTGT
66 TTAATTCAG-AAAAAAT-AAAAAACAATATTAGAAGCAAGAAAATCCCATCAATCTTTTTGGCGT
* * * * **
2395 TGAATTATATA-TTTTTCTGAGTATCGTGGCAAAAAATTGAGAAAAAAAAATTTCAGATCAGTTT
129 AGAATTATATATTTTTTCTGAGTATCGTGGCAAAAAATTGAG--AAAAACATTTCGGGTCAAATT
* * * * *
2459 TTAGCTGAAATCGTGGACTAACCATCATGGTTTTAGGCCT-AAAACGCTTTTCTAGGCCCCGACT
192 TTAGCTGAAATCGTGTACTAA--ATCACGGTTTT-TGCCTAAAAACGCGTTTCGA-GCCCCGACT
* * * * * * *
2523 TAGTTTTGCATGATTTTTGGCAGAAAGATTCCTTGAAATATCTATATTTATCTAACAAAATCTTA
253 TAGTTTTGCATGGTTTTTGGCAGAAAAACTACTTGAAATATCTATAATCATCTAACAAAATCTCA
*
2588 GCCACATTGTATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
318 GCCACATTGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
** * * * *
2653 AAATTTAGAAAAACATAGGAAAACGATATTTGAAGCGTGAAAAAACCCCTCAAA--TTTTTGTCG
383 AAATTCGGAAAAAAAT-GGAAAACGATATTAGAAGCG-GGAAAAA-CCCTTAAATTTTTTTGTCG
* * ** ** *
2716 TTGAAGTACATATTTTTTCTGAATA-TAGTGCCAAAAAAAATTGAGGAAATTCTTTTCGGGTCAG
445 TTGAATTATATATTTTTTCTGAATATTA-TG--GTAAAAAATTGAGGAAAAACTATTCGGGTCAG
* * * *
2780 TTTTTGCAAAATTTTAGCCGAAATCTTGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTTCC
507 TTTTTGCAAAAATATAGCCGAAATCGTGTA-T-ACCATCACGGTTTTTTGCTAAAAACGCGTTCC
* ** * * *
2845 GCAG--CCA--C--GGTTG-A--A--TTTT--GC-AAGACTCCTCCAAATATTTATATTTATCGA
570 GGAGTCCCACTCAATTTTGCATGATTTTTTGCGCAAAGACTCCTCGAAATATCTATATTCATCGA
2896 ACCAAATCTC
635 ACCAAATCTC
* * * *
2906 AGCCACATTAGATATAAGGATTT-ATTTTACGAGCATCTGAATTTTGTTTCGATTAAATTAGAAA
1 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
** *
2970 TTAATTCAGAGAAAAATCAAAAAACAATATTAGAAGCGTGAAAATCCTGA-CAATCTTTTTGGCG
66 TTAATTCAGA-AAAAAT-AAAAAACAATATTAGAAGCAAGAAAATCC-CATCAATCTTTTTGGCG
* * * *
3034 TAGAATTATGTATTTTTTCTGAGTATTGTGGCAAAGAATTGAGAAAAA-AGTTTTCGCGTC-AAT
128 TAGAATTATATATTTTTTCTGAGTATCGTGGCAAAAAATTGAGAAAAACA--TTTCGGGTCAAAT
* * * * * *
3097 TCTTAGCTGAAATCGTG---TAAGTTACGATTTTTTCCTAAAAACACGTTTCGAG-GCC-ACTCT
191 T-TTAGCTGAAATCGTGTACTAAATCACGGTTTTTGCCTAAAAACGCGTTTCGAGCCCCGACT-T
* * * * * *
3157 CAGTTTTGCATGGTTTTTGACATATAAACTACTTGAAATATCTAAAATCATCTAACCAAATATCA
254 -AGTTTTGCATGGTTTTTGGCAGAAAAACTACTTGAAATATCTATAATCATCTAACAAAATCTCA
* * *
3222 GCGACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTA-AAA-
318 GCCACATTGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * * *
3285 AATTATTTGGAAAAAAAGGGAAAACTG-TATTAGAAGCGTGAAAAATCCTTAAACTTTTTTGGT-
383 AA--ATTCGGAAAAAAATGGAAAAC-GATATTAGAAGCGGGAAAAACCCTTAAA-TTTTTTTGTC
* * *
3348 GTTGAATTATATAATTTTTCTGAATATTGTTGTAAAAAATTGAGGAAAAACTATTCGGGTCAGTT
444 GTTGAATTATATATTTTTTCTGAATATTATGGTAAAAAATTGAGGAAAAACTATTCGGGTCAGTT
**
3413 TTTGCAAAAATAT-GCCTGAAATC--G--TACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGA
509 TTTGCAAAAATATAGCC-GAAATCGTGTATACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGA
* * * ** * *
3473 GTCCCGACTCAATTTTGCAAGATTTTTGGCACAAAGGTTCCTTGAAATTTCTATATTCATCGAAC
573 GTCCC-ACTCAATTTTGCATGATTTTTTGCGCAAAGACTCCTCGAAATATCTATATTCATCGAAC
3538 CAAATCTC
637 CAAATCTC
* * **
3546 AGCTACA-TGAGATTTAA-GATTTGTTTTTACGTCCATCTGAATCTTGTTTCGATTTAATTAGAA
1 AGCCACATTG-GATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * * **
3609 ATTAATTCATAAAAAATGAAAAAAAACGATATTAGAAACAAGAAAATCCCATCAATCTTTTCCGC
65 ATTAATTCAGAAAAAAT---AAAAAACAATATTAGAAGCAAGAAAATCCCATCAATCTTTTTGGC
* * *
3674 GTTA-AATTATATATTTTTTATGAGTATCGTAGCAAAAAAATTGATAAAAACATTTCGGGTCAAA
127 G-TAGAATTATATATTTTTTCTGAGTATCGTGGC-AAAAAATTGAGAAAAACATTTCGGGTCAAA
* * * * *
3738 TTTTAGGC-AAAATCGAGTACTAACCATCACGGTTTATGGCTAGAAACGCGTTTCGGAGCCCCGA
190 TTTTA-GCTGAAATCGTGTACTAA--ATCACGGTTTTTGCCTAAAAACGCGTTTC-GAGCCCCGA
* * * * * * * *
3802 CTTAGTTTTGCTTGTTTTTTAGTAGAAAGACTA-TTTATAATATCTATATTCATCTAACTAAATC
251 CTTAGTTTTGCATGGTTTTTGGCAGAAAAACTACTTGA-AATATCTATAATCATCTAACAAAATC
* * * * *
3866 TCAGCCACATTGTATTTAAGAATTTGGTTTTACAATCATCTGAATCTTATTTCGATTTAATTAGA
315 TCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* *
3931 AATAAATTCGGAAAAACATGGAAAACGATATTAGAAGCGGGAAAAACCCTTCAATTTTTTTGTCG
380 AATAAATTCGGAAAAAAATGGAAAACGATATTAGAAGCGGGAAAAACCCTTAAATTTTTTTGTCG
* * * * * * *
3996 TTGAATTATATATATATTTTCTGAGTACTATGGTAAAAAATTGAGGAAAAGCTTTTCAGGTAAAT
445 TTGAATTATATAT-T-TTTTCTGAATATTATGGTAAAAAATTGAGGAAAAACTATTCGGGTCAGT
* * * * * **
4061 TCTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGATTTTTTGCT-AAAACTTGTTCCG
508 TTTTGCAAAAATATAGCCGAAATCGTGTA-T-ACCATCACGGTTTTTTGCTAAAAACGCGTTCCG
* * * *
4125 GAGCCCCAACTTAATTTTGCATGATTTTTTGCGCAAAGTCTCCTCAAAATATCTATATTCATCGA
571 GAGTCCC-ACTCAATTTTGCATGATTTTTTGCGCAAAGACTCCTCGAAATATCTATATTCATCGA
4190 ACCAAATCTC
635 ACCAAATCTC
* **
4200 AGCCACATTGGATATAAGGATTTG-TTTTACGAGAATCTGAATAATGTTTCGATTTAATTAGAAA
1 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
** ** *
4264 TTAATTTGGAAAAAATATGGAAAAACAATATTAGAAGCGTGAAAAT-CCAGTCAGTCTTTTTGGC
66 TTAATTCAGAAAAAATA---AAAAACAATATTAGAAGCAAGAAAATCCCA-TCAATCTTTTTGGC
* * * *
4328 GTAGAATTATTTATTTTTTCTGAGTATCGTGGCAAAAAATTGAGAAAATGC-TTTCGTGTCAATT
127 GTAGAATTATATATTTTTTCTGAGTATCGTGGCAAAAAATTGAGAAAA-ACATTTCGGGTCAAAT
*
4392 TTTAGCTGAAATCGTGTACGT---T-ACGGTTTTTGCCTAAAAACGCGTTTCGGAGCCCCGACTC
191 TTTAGCTGAAATCGTGTAC-TAAATCACGGTTTTTGCCTAAAAACGCGTTTC-GAGCCCCGACTT
* *
4453 AGTTTTGCATGGTTTTTGGCATAAAAACTACTTGAAATATCTATAATCATCTAACCAAATCTCAG
254 AGTTTTGCATGGTTTTTGGCAGAAAAACTACTTGAAATATCTATAATCATCTAACAAAATCTCAG
* *
4518 CCACATTGGATTTTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
319 CCACATT-G-TATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* *** * ** *
4583 TAAGTTTTTTTTTTAAAAAAA--GAAAACAAT-TTCAGAAGCATGAAAAACCCTTTAATTTTTTT
382 TAA-----ATTCGGAAAAAAATGGAAAACGATATT-AGAAGCGGGAAAAACCCTTAAATTTTTTT
* * * *
4645 CG-CGTTGAATTATATATTCTTT-TGAGTATTATGGTAAAGAATTGCGGAAAAA
441 -GTCGTTGAATTATATATTTTTTCTGAATATTATGGTAAAAAATTGAGGAAAAA
4697 AAATTTTGGG
Statistics
Matches: 1975, Mismatches: 328, Indels: 234
0.78 0.13 0.09
Matches are distributed among these distances:
625 32 0.02
626 3 0.00
627 2 0.00
628 31 0.02
629 11 0.01
630 113 0.06
631 56 0.03
632 29 0.01
633 48 0.02
634 130 0.07
635 19 0.01
637 6 0.00
638 53 0.03
639 236 0.12
640 162 0.08
641 150 0.08
642 27 0.01
643 62 0.03
644 5 0.00
646 34 0.02
647 157 0.08
648 101 0.05
649 69 0.03
650 79 0.04
651 6 0.00
652 7 0.00
653 93 0.05
654 220 0.11
655 34 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (644 bp):
AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
TTAATTCAGAAAAAATAAAAAACAATATTAGAAGCAAGAAAATCCCATCAATCTTTTTGGCGTAG
AATTATATATTTTTTCTGAGTATCGTGGCAAAAAATTGAGAAAAACATTTCGGGTCAAATTTTAG
CTGAAATCGTGTACTAAATCACGGTTTTTGCCTAAAAACGCGTTTCGAGCCCCGACTTAGTTTTG
CATGGTTTTTGGCAGAAAAACTACTTGAAATATCTATAATCATCTAACAAAATCTCAGCCACATT
GTATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG
AAAAAAATGGAAAACGATATTAGAAGCGGGAAAAACCCTTAAATTTTTTTGTCGTTGAATTATAT
ATTTTTTCTGAATATTATGGTAAAAAATTGAGGAAAAACTATTCGGGTCAGTTTTTGCAAAAATA
TAGCCGAAATCGTGTATACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGTCCCACTCAATT
TTGCATGATTTTTTGCGCAAAGACTCCTCGAAATATCTATATTCATCGAACCAAATCTC
Found at i:4743 original size:90 final size:90
Alignment explanation
Indices: 4639--4806 Score: 223
Period size: 90 Copynumber: 1.9 Consensus size: 90
4629 ACCCTTTAAT
* * * *
4639 TTTTTTCGCGTTGAATTATATA-TTCTTT-TGAGTATTATGGTAAAGAATTGCGGAAAAAAAATT
1 TTTTTTCGCATTGAATTATATACTT-TTTCTGAGTATTATGGCAAAAAATTGAGGAAAAAAAA-T
*
4702 TTGGGTCAATTTTTGTTTCAAGGAGTC
64 TCGGGTCAATTTTTGTTTCAAGGAGTC
* * **
4729 TTTTTTGGCATTGAATTATATACTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTATTC
1 TTTTTTCGCATTGAATTATATACTTTTTCTGAGTATTATGGCAAAAAATTGAGGAAAAAAAATTC
4794 GGGTCAATTTTTG
66 GGGTCAATTTTTG
4807 CAAAAACATT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
90 38 0.57
91 29 0.43
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (90 bp):
TTTTTTCGCATTGAATTATATACTTTTTCTGAGTATTATGGCAAAAAATTGAGGAAAAAAAATTC
GGGTCAATTTTTGTTTCAAGGAGTC
Found at i:6221 original size:326 final size:321
Alignment explanation
Indices: 4876--6709 Score: 1167
Period size: 319 Copynumber: 5.7 Consensus size: 321
4866 CCCGACTCAA
* * ** * * * * **
4876 TTTTGCAAGATTTTTGCCGAAATCATGAACTAATCATCACGATTTTTTGCTAAAAACGCGTTCCA
1 TTTTGCAAAAATTTTGCAAAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGC-TT-TT
** * * *
4941 GAACCCCGACTCAATTTTGCATGATTTTTGGC-GCAAAAGACTCCTCGGATTATCTATATTCATC
64 G-GGCCCGACTCAATTTTGCATGATTTTTGGCAG--AAAGACTCCTTGAAATATCTATATTCATC
* * * * * * * * *
5005 GAAGCAAATCTCAGCCACATTGGATATAAGGATTCG-TTTTACGAGCATCTGAATGTTGTTTCGA
126 TAACCAAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACGACCATCTAAATCTTATTTCGA
* * * * * * ** *
5069 TTTAATT-AAAATAAATTCAG-AAAAAATGGAAAAACAATATCAGAAGCGTGAAAATGCCGTCAA
191 TTTAATTAAAAAT-AATTCGGAAAAAAATGAAAAAACGATATTAGAAACATGAAAAACCCTTCAA
* * * *
5132 TCTTTTTGGCGTTGAATTATATTTTTTTTCAGAGTATTGTGGTAAAAAATTGA-GAATAAGA-TT
255 TC-TTTT-GTGTTGAATTATA--TATTTT---ATTATTGTGGCAAAAAATTGAGGAA-AA-ACTT
*
5195 TTC-GCGTCAAT
311 TTCAG-GTCAGT
* * *
5206 TTTTAGC--------TG---AAATTGTGTACTAACCATCACGGTTTTTTGGCTAAAAATG-TGTC
1 TTTT-GCAAAAATTTTGCAAAAATCGTGTACTAACCATCAC-GATTTTTGGCTAAAAACGCT-T-
* * ** * *
5259 TCGAGGCCCTGGCTCTGTTTTGCATTATTTTTGGCAGAAAGACTCCTTGAAATGTCTATATTCAT
62 TTG-GGCCC-GACTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCAT
* * * * * *
5324 CTAACCAAATC-ACAGGCAAATTGGATTTAAGGATTTGTTTCTACGAGCATATGAATCTTATTTC
125 CTAACCAAATCTA-AGCCACATTGGATTTAAGGATTTGTTTTTACGACCATCTAAATCTTATTTC
* *
5388 GATTTAATTAAAAATAAATTCGGAAAAAAATG-AAAAACGATATTAGAAGCATGAAAACCCCTTC
189 GATTTAATTAAAAAT-AATTCGGAAAAAAATGAAAAAACGATATTAGAAACATGAAAAACCCTT-
* * * *
5452 CATTTTTTTGGTGTTGAATTATATATATTTTCTGAATATTGTGGCAAAAAATTGAGGAAAAACTA
252 CAATCTTTT-GTGTTGAA-T-TATATA-TTT-T-ATTATTGTGGCAAAAAATTGAGGAAAAACTT
5517 TTCAGGTCAGT
311 TTCAGGTCAGT
* * * * *
5528 TTTTGCAAAAATATAGCAAAAATCGTG------CCATCACGGTTTTTTGCTAAAAATGC-TTT--
1 TTTTGCAAAAATTTTGCAAAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTTGG
* * * * *
5584 --CCGACTCAATTTTGCAAGATTTTTGGCACAAAGGCTCCTTGAAATTTCTATATTCATCGAACC
66 GCCCGACTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACC
* * * *
5647 AAATCTTAGCTACATGGGATTTAA-GATTTGTTTTTAC-ATCCATCTAAATCTTGTTTCGATTTA
131 AAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACGA-CCATCTAAATCTTATTTCGATTTA
* * * * *
5710 ATTAAAAATTAATTCAGAAAAAAAATTGAAAAAACGATATTGGAAACAAG-AAAATCTTATCAAT
195 ATTAAAAA-TAATTC-GGAAAAAAA-TGAAAAAACGATATTAGAAACATGAAAAACCCT-TCAAT
* * *
5774 CTTTTTGGAGTTGAATTATATATTTTTTTTGAGTATCGTGGCAAAAAATTGA-CACAAAACTTTT
256 C-TTTT-GTGTTGAATTATATA-TTTTATT-A-T-T-GTGGCAAAAAATTGAGGA-AAAACTTTT
*
5838 CAGGTCAAT
313 CAGGTCAGT
* ** ** * **
5847 TTGTGTC-AATTTTTTGCCGAAATCGTGTACTAACCATCA-TAGTTTTTGGCTTGAAACGCGTTT
1 TTTTG-CAAAAATTTTGCAAAAATCGTGTACTAACCATCACGA-TTTTTGGCTAAAAACGC-TTT
* * * * * * *
5910 TGGGGCCCCAACTTAGTTTTACATGATTTTTGACAGAAAGACTCCTTGTAATATCTATATTTATC
63 T-GGG-CCCGACTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATC
* * * * * *
5975 TAACCAAATCTCAAG-TACATTGTATTTAAGAATGTGTTTTTATGACCATTTAAATCTTATTTCG
126 TAACCAAATCT-AAGCCACATTGGATTTAAGGATTTGTTTTTACGACCATCTAAATCTTATTTCG
* * * *
6039 ATTTAATTAGAAATACATTCGGAAAAACATGGAAAAACGATATTAGAAACGTGAAAAACCCTTCA
190 ATTTAATTAAAAATA-ATTCGGAAAAAAATGAAAAAACGATATTAGAAACATGAAAAACCCTTC-
* *
6104 AATCTTTTGTCGTTGAATTATATA-TTTATTATTGCGGCAAAAAATTGAGGAAAAACTTTTCGGG
253 AATCTTTTGT-GTTGAATTATATATTTTATTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGG
*
6168 TTAGT
317 TCAGT
* *
6173 TTTTGCAAAAATTTTGCTAAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCATTCTG
1 TTTTGCAAAAATTTTGCAAAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGC-TTTTG
* * * *
6238 GAGTCCTGGCTCAATTTTGCATGATATTTGTTGCA-AAA-ACTCCTTGAAATATCTATATTTATC
65 G-G-CCCGACTCAATTTTGCATGAT-TTT-TGGCAGAAAGACTCCTTGAAATATCTATATTCATC
* * ** ** * * * *
6301 AAACCAAATCTTAGCCACATTGGATAGAAGGATTTGTTTTTACGTGCATCTGAATATTGTTTTGA
126 TAACCAAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACGACCATCTAAATCTTATTTCGA
* * * * *
6366 TTTAATTACAAATTTATTCGGAAAAAAATGAAAAAACGATATTAGAAAAAATG--AAATCATGTC
191 TTTAATTA-AAAATAATTCGGAAAAAAATGAAAAAACGATATTAG-AAACATGAAAAACCCT-TC
* * * * * * *
6429 AATCTTTTGGCGTTG-ATTATGTTTTTTTGGAGTATCGTGGCGAAAAATTGAGAAAAAAACTTTT
253 AATCTTTT-GTGTTGAATTAT-ATATTTT--ATTATTGTGGCAAAAAATTGAG-GAAAAACTTTT
6493 C-GAGTCAG-
313 CAG-GTCAGT
** * * *
6501 TTTT-----AA----GCCGAAATCGTGTACTAACCATCATGGTTTTTGGCAAAAAACG-TGTTTC
1 TTTTGCAAAAATTTTGCAAAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCT-TTT-
* * * * * * * * *
6556 GGGGCCTCGACTCAGTTTTGCATGGTTTTTGGTATAAAGTA-TCCTTCAAATATATTTAATCATT
64 -GGGCC-CGACTCAATTTTGCATGATTTTTGGCAGAAAG-ACTCCTTGAAATATCTATATTCATC
* * * *
6620 TAACCAAATCTCAA-CCACATTGGATTTATGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
126 TAACCAAATCT-AAGCCACATTGGATTTAAGGATTTGTTTTTACGACCATCTAAATCTTATTTCG
* *
6684 ATTTAATTAGAAATAAATTCAGAAAA
190 ATTTAATTAAAAAT-AATTCGGAAAA
6710 GCATGG
Statistics
Matches: 1196, Mismatches: 217, Indels: 193
0.74 0.14 0.12
Matches are distributed among these distances:
315 2 0.00
316 47 0.04
317 94 0.08
318 28 0.02
319 224 0.19
320 82 0.07
321 70 0.06
322 86 0.07
323 24 0.02
324 11 0.01
325 58 0.05
326 214 0.18
327 20 0.02
328 27 0.02
329 17 0.01
330 9 0.01
331 3 0.00
332 46 0.04
333 88 0.07
334 45 0.04
335 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (321 bp):
TTTTGCAAAAATTTTGCAAAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTTGG
GCCCGACTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACC
AAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACGACCATCTAAATCTTATTTCGATTTAA
TTAAAAATAATTCGGAAAAAAATGAAAAAACGATATTAGAAACATGAAAAACCCTTCAATCTTTT
GTGTTGAATTATATATTTTATTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAGT
Done.